by Brent Schrotenboer, USA TODAY Sports

by Brent Schrotenboer, USA TODAY Sports

NCAA President Mark Emmert has a special relationship with Alabama head football coach Nick Saban.

As chancellor at LSU from 1999 to 2004, Emmert hired Saban as his football coach and eventually helped make him the highest-paid coach in the nation at $2.3 million.

"Chancellor Emmert is absolutely the best boss I've ever had," Saban said at LSU in 2004. "He's the most significant reason I was interested in the job. Never once has he disappointed me."

But how will that relationship work out now?

Saban's program at Alabama has a problem that might draw attention from Emmert's NCAA. According to a recent report by Yahoo Sports, one of Saban's best players, D.J. Fluker, took money and gifts at Alabama in 2012 - a possible rules violation that could draw a penalty as serious as ordering Alabama to vacate last season's national title. An assistant Alabama strength coach also recently was placed on leave for providing an impermissible short-term loan to a football player, according to The Tuscaloosa News.

It's another tough spot for the NCAA. Not only are its rules of amateurism under attack in federal court, but cases like this also present a recurring challenge to the organization's image - the perception of bias when enforcing those rules. Close relationships among power brokers fuel that perception, especially because NCAA justice is meted out by peers in the small world of college sports. The perception grows when justice seems to be handled differently for different schools. In the past few years, the NCAA has faced criticism about how it punished - or didn't punish - various schools compared to others, including Penn State, Southern California and a pending case at Miami (Fla.).

Alabama has two perceived friends in high places: Emmert and Alabama graduate Derrick Crawford, a director of enforcement for the NCAA. In the outside world, it's akin to being accused of a crime and having the charges investigated at the police station where your uncle is the police chief and your friend is the top detective.

"That's why (the NCAA) probably will handle this case very carefully - because of the perception," said Michael Buckner, a private attorney in Miami who specializes in NCAA cases. "They're probably going to err on the side of caution, so that nothing they do could be seen as being improper."

Alabama did not respond to numerous requests for comment. The NCAA said it does not comment on current or potential investigations, but said it has a system of checks and balances to avoid conflicts.

"If an enforcement staff member or leadership, Committee on Infractions member or even the association president has any connection with a member school under investigation, that person is immediately recused from the case and has absolutely no role with either investigating or deciding penalties for that infractions case," NCAA spokeswoman Emily Potter told USA TODAY Sports in a statement.

Yet others point out that the lines between recusal and indirect involvement have gotten so blurry at times that perceptions of bias easily can trump reality, harming the NCAA's credibility, fairly or not.

"There are ex-parte conversations about cases, friends talking to friends and outside influences," said David Ridpath, a frequent NCAA critic and president-elect of the Drake Group, which seeks reform in college sports. "Despite the NCAA's denial, it does happen and adds to the tremendous flaws and unfairness of the system."

The NCAA's official stance is that its president stays above the fray of individual enforcement cases. If he got involved in them, he'd open himself up to charges of bias, politics and improper influence.

"The president of the NCAA doesn't get involved in infractions cases," Emmert told USA TODAY Sports this year. "That's one of those mythologies out there."

Yet the NCAA acknowledges Emmert has put himself in the middle of a few high-profile cases. He led the charge in slamming Penn State with harsh penalties for the child sex-abuse crimes committed by former assistant football coach Jerry Sandusky. Emmert also publicly criticized his enforcement staff this year for tactics it used to gather evidence in the pending investigation against Miami, calling the situation an embarrassment. His vice president of enforcement was fired.

"The NCAA has a major credibility problem when it comes to enforcement actions, and that's especially so under Mark Emmert because it seems Emmert picks and chooses when he wants to get involved," said Stephen Miller, an attorney in Philadelphia who has represented college athletes in disputes with the NCAA. "He doesn't get involved in investigations - except when he does."

Higher profile

Compared to his two predecessors, Emmert "definitely has gotten more involved in making public comments about cases," said Gene Marsh, former chairman of the NCAA infractions committee. "That's a fact."

The NCAA's process works like this: After learning of potential rules violations, the enforcement staff conducts an investigation before sending the case to the infractions committee, which acts as judge and jury in determining penalties. Current and former officials from various schools and conferences serve on that committee, sitting in judgment of their peers in college sports.

In the Penn State case, however, Emmert sent a letter with questions to the Penn State president shortly after allegations of Sandusky's crimes became public.

"As you and I have discussed, it is essential for Penn State to respond to the questions I have posed so that any failures in the management of athletics programs - both perceived and real - can be rectified," Emmert wrote to Rodney Erickson in November 2011.

Eight months later, Emmert announced the Penn State sanctions - a function that is usually is handled by the NCAA infractions committee. The NCAA said the exceptional nature of the Penn State case prompted it to bypass its normal process.

Likewise, it said Emmert's involvement in the Miami case came after questions arose about the ethics of the NCAA's investigative tactics.

A few weeks ago, USC athletics director Pat Haden also met with Emmert and other NCAA officials. "During our meetings with the NCAA's leaders â?¦ we discussed enforcement and sanction issues impacting both the NCAA membership at large and USC specifically," Haden said in a statement.

Haden wanted the NCAA to consider softening the penalties it handed down in the case involving former USC running back Reggie Bush. Haden said he considered the severe penalties to be inconsistent with similar cases. The NCAA turned him down. NCAA officials said USC brought up the topic of sanctions during a meeting that involved other topics, too.

Neutrality questions

As for Alabama, Crawford would be expected to recuse himself by rule. Yet no matter how the NCAA handles the case, other schools and their fans likely will perceive it as favoritism if Emmert's NCAA can't prove the allegations or doesn't punish Alabama enough to their liking.

Rival fans already suspected Alabama of getting a free pass when the school dissociated itself from a local store owner and told him to stop selling or distributing items autographed by current Alabama players. Alabama said it didn't find evidence that its players received anything impermissible in return for any autographs.

Miller, the attorney, said the system has "built-in, inherent conflicts of interest" and has called for the NCAA to outsource its investigations to independent agencies or law firms. He predicts major schools will want to break away from the NCAA because "it's no longer worth it to be subject to that kind of arbitrary enforcement."

"You have competitors and friends of programs serving as prosecutor, judge and jury," Miller said. "How can anyone have faith in the neutrality of that system?"

Such relationships have raised questions in the past.

In 2010, The News & Observer in Raleigh, N.C., reported that NCAA investigator Marcus Wilson, a former North Carolina football player, interviewed South Carolina player Weslye Saunders about his relationship with a North Carolina player - Marvin Austin, who was under NCAA investigation for taking improper benefits from an agent. "Even him looking at a file is improper," Ridpath said.

NCAA spokeswoman Stacey Osburn maintained Wilson was not involved with a North Carolina case.

Recused but involved

Alabama also faced a similar issue in a previous case.

From 1999 to 2008, Marsh, a longtime faculty member at Alabama, served as a member of the NCAA infractions committee. Marsh recused himself from a case in 2001 and 2002, when Alabama football was under investigation for having boosters pay for recruits.

But as Alabama's faculty athletics representative, Marsh acknowledged he remained involved, helping Alabama with rules compliance and cooperation with the NCAA.

In the end, the NCAA hit Alabama with penalties that included a two-year postseason ban, five years probation and the loss of 21 scholarships. Yet Tom Yeager, then-chairman of the infractions committee, declared that it could have been worse if not for Marsh and Alabama's compliance director, Marie Robbins.

The efforts of Marsh and Robbins "not only saved the university from the death penalty but also more serious sanctions that would have been imposed," Yeager said then.

Marsh told USA TODAY Sports he was not involved in the judicial part of that case, and only helped Alabama follow the rules and cooperate with NCAA staff. He said Yeager apologized profusely for making that comment about him.

Marsh caught blowback from both directions: Alabama fans thought he didn't do enough to prevent harsh sanctions. Others wondered if he used his committee influence to save Alabama from even harsher punishment.

"Among reasonable people, it would be viewed as a good thing if you saved a school from getting the death penalty, but somebody looking at it from another angle might think maybe that was a favor," Marsh said. "But I promise you that is not the way it worked."